def grep(fileName, txt, resultList = None, doQuiet=False, caseSensitive=True):
"""
Exit status is 0 if selected lines are found and 1 if none are found.
Exit status 2 is returned if an error occurred, unless the -q or --quiet or --silent option is used and a selected line is found.
Instead of printing, a resultList will be filled if provided.
"""
if not os.path.exists(fileName):
return 2
if not caseSensitive:
txt = txt.lower()
matchedLine = False
for line in open(fileName):
if len(line):
line = line[:-1] # must be at least 1 char long
else:
nTcodeerror("Fix code in grep")
lineMod = line
if not caseSensitive:
lineMod = lineMod.lower()
if txt in lineMod:
# nTdebug("Matched line in grep: %s" % lineMod)
if resultList != None:
resultList.append(line)
if doQuiet:
# important for not scanning whole file.
return 0
matchedLine = True
if matchedLine:
return 0
return 1
def grep(fileName, txt, resultList=None, doQuiet=False, caseSensitive=True):
"""
Exit status is 0 if selected lines are found and 1 if none are found.
Exit status 2 is returned if an error occurred, unless the -q or --quiet or --silent option is used and a selected line is found.
Instead of printing, a resultList will be filled if provided.
"""
if not os.path.exists(fileName):
return 2
if not caseSensitive:
txt = txt.lower()
matchedLine = False
for line in open(fileName):
if len(line):
line = line[:-1] # must be at least 1 char long
else:
nTcodeerror("Fix code in grep")
lineMod = line
if not caseSensitive:
lineMod = lineMod.lower()
if txt in lineMod:
# nTdebug("Matched line in grep: %s" % lineMod)
if resultList != None:
resultList.append(line)
if doQuiet:
# important for not scanning whole file.
return 0
matchedLine = True
if matchedLine:
return 0
return 1
def _restoreFromSML(self, convention=constants.INTERNAL):
"""
Restore the MolDef instance from CING ResidueDef SML files
"""
rootPath = os.path.realpath(os.path.join(cingPythonCingDir, "Database", convention))
if not os.path.exists(rootPath):
nTcodeerror('MolDef._restoreFromSML: rootPath "%s" does not exist; bailing out!', rootPath)
sys.exit(1)
# end if
restoreFromSML(rootPath, self, convention=convention)
self.postProcess()
return NTdb
def capitalizeFirst(s):
if s == None:
return
# end if
if not isinstance(s, str):
nTcodeerror('Failed capitalizeFirst with non string argument: [%s]' % str(s))
return
# end if
if len(s) < 1:
return ''
# end if
firstChar = s[0].capitalize()
if len(s) == 1:
return firstChar
# end if
return firstChar + s[1:]
def capitalizeFirst(s):
if s == None:
return
# end if
if not isinstance(s, str):
nTcodeerror('Failed capitalizeFirst with non string argument: [%s]' %
str(s))
return
# end if
if len(s) < 1:
return ''
# end if
firstChar = s[0].capitalize()
if len(s) == 1:
return firstChar
# end if
return firstChar + s[1:]
def getAtomDefByName(self, atmName, convention=constants.INTERNAL):
"""return AtomDef instance for atmName if atmName is a valid for convention
or None otherwise.
Do NOT print an error here because for optimal use the code is called
many times in cases where no defs are available; e.g.
pdbParser#_matchAtom2Cing
"""
if not atmName:
nTcodeerror("ResidueDef.getAtomDefByName: atmName not defined")
return None
# end if
if not self.atomDict.has_key(convention):
# nTdebug('ResidueDef.getAtomDefByName: convention %s not defined within CING', convention)
return None
# end if
an = atmName.strip()
if self.atomDict[convention].has_key(an):
return self.atomDict[convention][an]
# endif
return None
